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annotate join.xml @ 3:ffbd1de29c28 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:48:58 -0500 |
| parents | de21bdbb8d28 |
| children | a10f49d9218a |
| rev | line source |
|---|---|
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11a49f94d086
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
0
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changeset
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1 <tool id="gops_join_1" name="Join" version="1.0.0"> |
| 0 | 2 <description>the intervals of two datasets side-by-side</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python">gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill</command> | |
| 8 <inputs> | |
| 9 <param format="interval" name="input1" type="data" help="First dataset"> | |
| 10 <label>Join</label> | |
| 11 </param> | |
| 12 <param format="interval" name="input2" type="data" help="Second dataset"> | |
| 13 <label>with</label> | |
| 14 </param> | |
|
3
ffbd1de29c28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
2
diff
changeset
|
15 <param name="min" type="integer" value="1" help="(bp)"> |
| 0 | 16 <label>with min overlap</label> |
| 17 </param> | |
| 18 <param name="fill" type="select" label="Return"> | |
| 19 <option value="none">Only records that are joined (INNER JOIN)</option> | |
| 20 <option value="right">All records of first dataset (fill null with ".")</option> | |
| 21 <option value="left">All records of second dataset (fill null with ".")</option> | |
| 22 <option value="both">All records of both datasets (fill nulls with ".")</option> | |
| 23 </param> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="interval" name="output" metadata_source="input1" /> | |
| 27 </outputs> | |
| 28 <code file="operation_filter.py"/> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="input1" value="1.bed" /> | |
| 32 <param name="input2" value="2.bed" /> | |
| 33 <param name="min" value="1" /> | |
| 34 <param name="fill" value="none" /> | |
| 35 <output name="output" file="gops-join-none.dat" /> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input1" value="1.bed" /> | |
| 39 <param name="input2" value="2.bed" /> | |
| 40 <param name="min" value="1" /> | |
| 41 <param name="fill" value="right" /> | |
| 42 <output name="output" file="gops-join-right.dat" /> | |
| 43 </test> | |
| 44 <test> | |
| 45 <param name="input1" value="1.bed" /> | |
| 46 <param name="input2" value="2.bed" /> | |
| 47 <param name="min" value="1" /> | |
| 48 <param name="fill" value="left" /> | |
| 49 <output name="output" file="gops-join-left.dat" /> | |
| 50 </test> | |
| 51 <test> | |
| 52 <param name="input1" value="1.bed" /> | |
| 53 <param name="input2" value="2.bed" /> | |
| 54 <param name="min" value="1" /> | |
| 55 <param name="fill" value="both" /> | |
| 56 <output name="output" file="gops-join-both.dat" /> | |
| 57 </test> | |
| 58 <test> | |
| 59 <param name="input1" value="1.bed" /> | |
| 60 <param name="input2" value="2.bed" /> | |
| 61 <param name="min" value="500" /> | |
| 62 <param name="fill" value="none" /> | |
| 63 <output name="output" file="gops-join-none-500.dat" /> | |
| 64 </test> | |
| 65 <test> | |
| 66 <param name="input1" value="1.bed" /> | |
| 67 <param name="input2" value="2.bed" /> | |
| 68 <param name="min" value="100" /> | |
| 69 <param name="fill" value="both" /> | |
| 70 <output name="output" file="gops-join-both-100.dat" /> | |
| 71 </test> | |
| 72 </tests> | |
| 73 <help> | |
| 74 | |
| 75 .. class:: infomark | |
| 76 | |
| 77 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. | |
| 78 | |
| 79 ----- | |
| 80 | |
| 81 **Screencasts!** | |
| 82 | |
| 83 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). | |
| 84 | |
| 85 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations | |
| 86 | |
| 87 ----- | |
| 88 | |
| 89 **Syntax** | |
| 90 | |
| 91 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined. | |
| 92 - **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN. | |
| 93 - **Return all records of first dataset (fill null with ".")** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN. | |
| 94 - **Return all records of second dataset (fill null with ".")** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** | |
| 95 - **Return all records of both datasets (fill nulls with ".")** returns all records from both datasets, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** | |
| 96 | |
| 97 ----- | |
| 98 | |
| 99 **Examples** | |
| 100 | |
| 2 | 101 .. image:: gops_joinRecordsList.gif |
| 0 | 102 |
| 103 Only records that are joined (inner join): | |
| 104 | |
| 2 | 105 .. image:: gops_joinInner.gif |
| 0 | 106 |
| 107 All records of first dataset: | |
| 108 | |
| 2 | 109 .. image:: gops_joinLeftOuter.gif |
| 0 | 110 |
| 111 All records of second dataset: | |
| 112 | |
| 2 | 113 .. image:: gops_joinRightOuter.gif |
| 0 | 114 |
| 115 All records of both datasets: | |
| 116 | |
| 2 | 117 .. image:: gops_joinFullOuter.gif |
| 0 | 118 |
| 119 | |
| 120 </help> | |
| 121 </tool> |